Add more specific error messages to help debugging

[corneliusroemer]

When I include an invalid nucleotide in the root sequence, all I get is a fairly non-descriptive error message:

[ERROR] Nextclade: Error: Invalid nucleotide: "E"

It'd be helpful for users if the error message included the file (root seq) in which the invalid nucleotide was found, similar to how the same error in a sample sequence is reported:

[ WARN] Nextclade: Warning: In sequence "MK630463": Invalid nucleotide: "E". Note that this sequence will be excluded from results.